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As pchrist7 says, adding books to collections only changes the collections.json file. It does not update the metadata in books or change their titles or pathnames, etc. It does not change what is stored in calibre.
Whether a book shows up as on-device in Calibre has nothing to do with the plugin. If some books are not showing up as on-device that are really on the device, then I suggest you look at resolving this first before trying to resolve any collections issue.
The plugin gets the information about what is on device directly from calibre these days, and doesn't use the metadata.calibre file.
I wonder if renaming metadata.calibre (on the Kindle) and then restarting calibre to force it to rebuild metadata.calibre will help. Of course with 2000 books this could take a very long time! And if the calibre options are set as chaley described it might not change anything anyway.
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